How high up do you want to be? Do you want to be near mountains or do you want to be at elevation to get "altitude training"?
If you are not that worried about being too high up, you could check out Mt. Shasta, CA. or some of the lesser known surrounding towns. Kind of a lot of hippies and new agers up there, but it is beautiful. There is a decent running scene (at least last time I was there).
Eastern Sierra is really beautiful, but I'm not so much into the desert thing. I likes my mountains with trees. If you head to the west slope of the Sierra, you get a lot more snow, which hampers wintertime training, but there are lots of good smaller towns. Check out the Graeagal/Blairsden area north of Tahoe. It sits in a little valley, so a lot of the snow that would inhibit winter running is blocked by the range to the west. I want to say the elevation there is about 4500 feet, but you've go big peaks on all sides and excellent camping/hiking/running in the Gold Lakes basin not too far up the hill.